To achieve long exposures in daylight, one might need to stop down, or use an ND filter. By stopping down, the depth of field increases, but at some point the image quality/sharpness will suffer, due to diffraction. If one does not care about depth of field, and the same light attenuation can be achieved either via a ND filter or stopping down, is one to be preferred to another? Is there any cases where it could be a disadvantage to use an ND over stopping down?
There is a point where lenses transition from being aberration limited to being diffraction limited. This means that peak sharpness will increase up to a point as you stop down but will then start to decrease again. If you don't care about depth of field then use of an ND filter is preferable to stopping down past this point.
Of course ND filters aren't perfect and constitute another pair of surfaces to create reflections. So there is a small penalty for using an ND filter. Really powerful filters may also induce a slight colour cast as they are never perfectly neutral. So going slightly past the diffraction limit might be wise before getting out the ND filter. Vari-ND filters suffer from all the problems of a polarizing filter.
In reality you're probably going to stop down and use an ND to get the right shutter speed unless you have a huge number of different ND filters or a variable filter.
At least with diffraction you can do full-frame sharpening since the softness is distributed evenly...
Some disadvantages of an ND filter:
An ND filter adds another layer of glass to the lens and will increase the chance of flare, depending on the quality of the filter.
Strong ND filters on wide angle lenses can (because an extreme angle of view changes the effective thickness of filter) darken more towards the edges (vignette) than in the center.
Depending on the strength of the ND filter, the ability of the ND filter to block IR as well as visible light, and the effectiveness of the in-camera IR filter there may be a noticable IR leakage effect for very long exposures.
In quite a few cases ND filters can be a disadvantage. Filters cost money(especially high quality ones), they can appear in the frame, they require extra equipment(space, weight, time), they can introduce defects, etc. Another user has already pointed out why stopping down your aperture can cause problems.
In reality, it is hard to image when one would not care at all about the depth of field.